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Beta-diversity analysis

Where we analyse the effect of a factor on shared diversity

Author: Adrien Taudière

Date: December 2, 2024

See the documentation of the MiscMetabar package for example of btea diversity analysis.

Code 
if(base::interactive()) {
  params <- rmarkdown::yaml_front_matter(here::here("analysis/03_beta_diversity.qmd"))$params
}
factor_of_interest <- params$factor_of_interest
Code 
library(knitr)
library(targets)
library(MiscMetabar)
here::i_am("analysis/03_beta_diversity.qmd")
source(here::here("R/styles.R"))
Code 
d_pq <- clean_pq(tar_read("d_vs", store=here::here("_targets/")))
Cleaning suppress 0 taxa and 26 samples.
Code 
formattable_pq(
    subset_samples(d_pq, Type %in% c("Mix", "Mono")),
    factor_of_interest,
    min_nb_seq_taxa = 1000, 
    lev_col_taxa = "Family",
    taxonomic_levels=c("Order", "Family", "Genus"),
    log10trans = TRUE,

  )
Error in h(simpleError(msg, call)): erreur d'�valuation de l'argument 'x' lors de la s�lection d'une m�thode pour la fonction '%in%' : objet 'Type' introuvable
Code 
library("vegan")
Le chargement a nécessité le package : permute
Le chargement a nécessité le package : lattice
This is vegan 2.6-8
Code 
plot_ordination(d_pq, vegan::decorana(vegdist(as(otu_table(d_pq), "matrix"),
    method = "robust.aitchison"
  )), color = factor_of_interest) +
  geom_point(size = 3) +
  stat_ellipse(inherit.aes = F, aes(x = DCA1, y = DCA2, linetype = .data[[factor_of_interest]], col = .data[[factor_of_interest]])) + theme_idest() + scale_color_manual(values=idest_pal$dark_color_idest[[1]][c(5,4,2)])
Warning in plot_ordination(d_pq, vegan::decorana(vegdist(as(otu_table(d_pq), :
`Ordination species/OTU/taxa coordinate indices did not match `physeq` index
names. Setting corresponding coordinates to NULL.
Warning in plot_ordination(d_pq, vegan::decorana(vegdist(as(otu_table(d_pq), :
Color variable was not found in the available data you provided.No color
mapped.
Error in `stat_ellipse()`:
! Problem while computing aesthetics.
ℹ Error occurred in the 3rd layer.
Caused by error in `.data[["Type"]]`:
! Column `Type` not found in `.data`.
Code 
adonis_pq(subset_samples(d_pq, Type %in% c("Mix", "Mono")), factor_of_interest, na_remove = TRUE, correction_for_sample_size = TRUE, by = "terms")
Error in h(simpleError(msg, call)): erreur d'�valuation de l'argument 'x' lors de la s�lection d'une m�thode pour la fonction '%in%' : objet 'Type' introuvable
Code 
d_pq |>
  subset_samples(Type %in% c("Mix", "Mono")) |>
biplot_pq(merge_sample_by = factor_of_interest, rarefy_after_merging = T)
Error in h(simpleError(msg, call)): erreur d'�valuation de l'argument 'x' lors de la s�lection d'une m�thode pour la fonction '%in%' : objet 'Type' introuvable
Code 
res_var <- var_par_rarperm_pq(
    subset_samples(d_pq, Type %in% c("Mix", "Mono")),
    list_component = list(
      "Tmt" = c("Tmt"),
      "Bloc" = c("Bloc"),
      "Type" = c("Type")
    ),
    nperm = 9,
    dbrda_computation = TRUE
  )
Error in h(simpleError(msg, call)): erreur d'�valuation de l'argument 'x' lors de la s�lection d'une m�thode pour la fonction '%in%' : objet 'Type' introuvable
Code 
plot_var_part_pq(res_var)
Error: objet 'res_var' introuvable

Session Information

Session information are detailed below. More information about the machine, the system, as well as python and R packages, are available in the file data_final/information_run.txt .

Code 
sessionInfo()
R version 4.4.2 (2024-10-31)
Platform: x86_64-pc-linux-gnu
Running under: Debian GNU/Linux 12 (bookworm)

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.11.0 
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.11.0

locale:
 [1] LC_CTYPE=fr_FR.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=fr_FR.UTF-8        LC_COLLATE=fr_FR.UTF-8    
 [5] LC_MONETARY=fr_FR.UTF-8    LC_MESSAGES=fr_FR.UTF-8   
 [7] LC_PAPER=fr_FR.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C       

time zone: Europe/Paris
tzcode source: system (glibc)

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base     

other attached packages:
 [1] vegan_2.6-8        lattice_0.22-6     permute_0.9-7      MiscMetabar_0.10.1
 [5] purrr_1.0.2        dplyr_1.1.4        dada2_1.34.0       Rcpp_1.0.13-1     
 [9] ggplot2_3.5.1      phyloseq_1.50.0    targets_1.9.0      knitr_1.49        

loaded via a namespace (and not attached):
  [1] bitops_1.0-9                deldir_2.0-4               
  [3] rlang_1.1.4                 magrittr_2.0.3             
  [5] ade4_1.7-22                 matrixStats_1.4.1          
  [7] compiler_4.4.2              mgcv_1.9-1                 
  [9] png_0.1-8                   callr_3.7.6                
 [11] vctrs_0.6.5                 reshape2_1.4.4             
 [13] stringr_1.5.1               pwalign_1.2.0              
 [15] pkgconfig_2.0.3             crayon_1.5.3               
 [17] fastmap_1.2.0               backports_1.5.0            
 [19] XVector_0.46.0              utf8_1.2.4                 
 [21] Rsamtools_2.22.0            rmarkdown_2.29             
 [23] UCSC.utils_1.2.0            ps_1.8.1                   
 [25] xfun_0.49                   zlibbioc_1.52.0            
 [27] GenomeInfoDb_1.42.1         jsonlite_1.8.9             
 [29] biomformat_1.34.0           rhdf5filters_1.18.0        
 [31] DelayedArray_0.32.0         Rhdf5lib_1.28.0            
 [33] BiocParallel_1.40.0         jpeg_0.1-10                
 [35] parallel_4.4.2              cluster_2.1.6              
 [37] R6_2.5.1                    RColorBrewer_1.1-3         
 [39] stringi_1.8.4               GenomicRanges_1.58.0       
 [41] SummarizedExperiment_1.36.0 iterators_1.0.14           
 [43] IRanges_2.40.0              Matrix_1.7-1               
 [45] splines_4.4.2               igraph_2.1.1               
 [47] tidyselect_1.2.1            rstudioapi_0.17.1          
 [49] abind_1.4-8                 yaml_2.3.10                
 [51] codetools_0.2-20            hwriter_1.3.2.1            
 [53] processx_3.8.4              tibble_3.2.1               
 [55] plyr_1.8.9                  Biobase_2.66.0             
 [57] withr_3.0.2                 ShortRead_1.64.0           
 [59] evaluate_1.0.1              survival_3.7-0             
 [61] RcppParallel_5.1.9          Biostrings_2.74.0          
 [63] pillar_1.9.0                BiocManager_1.30.25        
 [65] MatrixGenerics_1.18.0       renv_1.0.11                
 [67] foreach_1.5.2               stats4_4.4.2               
 [69] generics_0.1.3              rprojroot_2.0.4            
 [71] S4Vectors_0.44.0            munsell_0.5.1              
 [73] scales_1.3.0                base64url_1.4              
 [75] glue_1.8.0                  tools_4.4.2                
 [77] interp_1.1-6                data.table_1.16.2          
 [79] GenomicAlignments_1.42.0    rhdf5_2.50.0               
 [81] grid_4.4.2                  ape_5.8                    
 [83] latticeExtra_0.6-30         colorspace_2.1-1           
 [85] nlme_3.1-166                GenomeInfoDbData_1.2.13    
 [87] cli_3.6.3                   fansi_1.0.6                
 [89] S4Arrays_1.6.0              gtable_0.3.6               
 [91] digest_0.6.37               BiocGenerics_0.52.0        
 [93] SparseArray_1.6.0           htmlwidgets_1.6.4          
 [95] htmltools_0.5.8.1           multtest_2.62.0            
 [97] lifecycle_1.0.4             here_1.0.1                 
 [99] httr_1.4.7                  secretbase_1.0.3           
[101] MASS_7.3-61

This document was made by the Adrien Taudière, whith multiple inspirations from the Lumo quarto template.